"I take it this is a new error for the series? I never witnessed this problem back on ARMA 2?"
It's a new problem in the sense that there are more commands with a global effect in use in Arma 3. In Arma 2 you would've gotten the same effect if you had used "(unitBackpack this) addMagazineCargoGlobal".
The issue is that to ensure the items go where the player wants, the Virtual Arsenal uses addItemToUniform/Vest/Backpack, which all work with global arguments and have a global effect. Without a locality check or a "do only once" variable check, this means duplicates when JIP is involved.
The commands for adding the uniforms, vests and backpacks themselves are global too, but it's not as big of a problem (addUniform was local previously, and that was terrible in another way when trying to setup loadouts).